I've greatly enjoyed free access for alpha and I hope some of my suggestions will be fruitful for you. :)

Building:

Storeys - I believe that to build cities people require to have an ability to make upper floors or even basements. Possibility to do something more with your house might prove bountiful for imagination. Even now, I have wished for storeys, So I could make beautiful slopes on my roof. :P

Resources - Though I believe you will add quite a lot, maybe this will be a good suggestion. Different kinds of woods - with their approperiate colours should influance colour of what we are building.

Paints - I don't have to write more :3

Gameplay:

Cursor & Crafting - When your mouse hovers over image of something in crafting menu, you receive an crude explanation of what it is and what it does. For example an oven: If you fancy baking a bread, then get a dough and put it in. - I know it sounds stupid, but it's late. :P

Cursor - If your dominion is full of everything that's - clickable, then you will have a lot of problems with moving around. Some hotkey that could let you just move, without performing any different action like gathering carrots would be awesome.

Cursor - If for example you wish to demolish something in house, your roof will always be in the way - this is why I believe that option to choose what you want to destroy, your old bed or slope would be extremely useful. Also ability to move and turn furniture around would be great.

Roofs - People love to have beautiful houses/bases, but when they go inside their houses, the whole roof which is connected, should fade or fully dissapear, when someone is inside. (Not just parts where character is, it looks unsightly.)

Resources- Purity indicator of an ore that would influance bar, then later statistics of item made from it. People would strive for best possible quality if it could make a difference.

Map - I am totally sure that you have plans to make some minimap. But I want to suggest a crude map, that would present whole world. But not in form of minimap, but a hotkey that shows a scroll. Later people could explore and craft improved maps.

World - Some buildings, lakes, just locations that could serve as orientation points for people. For example enormous rock, a mountain.

World - It would be awesome if some specific locations had abudance of certain rare resources. It could make people band together in order to gain full access to these resources. For example mine in which there are rare metals like mithril or something. :)
Of course I also believe there should be a lot of monsters, so players will have no choice but to work together.

Capacity - Limiting how much person can carry and enabling of crafting carts and such devices to overcome these limits.

Magic - Though I have no idea if you even consider adding this feature to the game, I believe it would be great addition to sandbox MMO. Especially if it would be based on some magic resources, like arcane ore.

Herbs - I believe there's a great potential for potions and poultices in this game.
People also travel a lot, so looking for herbs might be another fun thing to do.
There's a lot of potions that would be greatly useful, for example potion that slowly regenerates stamina, classic health potion or poisons that would serve as coating for weapons, corrosive liquids that would eat up walls.

Random events - From coordinated emigration of wolves through map to finding gem in dirt, when you're making a field. This is what makes people smile and wish for more, they love surprises.

Thanks for opinion, why do you think that crude map would be a bad idea though? I imagine that minimap would be a big handicap and game would lose a little bit of charm .:P
For some reason I couldn't find edit button, but I forgot to wrote down two more ideas.

View - It would be great if we could expand even for a moment how much we can see in game. :)
It could be even ability that consumes stamina, but I believe it would be very useful.

Communication - Even though chat will have for sure a lot of changes, what I wanted to inquire about is voice communication. If we could speak and hear in range of our screens it would be really great for just some random talking with neighbors and while crafting or foraging together. Of course with option on and off. :)

Cursor: If we could highlight what we are selecting. I encountered a lot of problems with efficiency while trying to get apples from my orchard, since it's hard to know which tree you're selecting.

Building: Ability to queue up crafting or building. For example I wasted soo much time waiting till some pave road will be complate, so I can begin building new one.
If we could just queue these up it would vastly improve efficiency.

Gameplay: I see tab with snares etc. Do they work on players though? Some traps against intruders would be great. But this isn't what I wanted to write about.
An ability to somehow detect, who ransacked your house would be great for revenge driven gameplay. I Would propose some magic, but if not, then I guess there should be different more normal option? Like NPC detective?